96ec9e39529c5b8340bcd38e377b208a *DESCRIPTION
8406fd1414247da7405904c2546ad3c6 *NAMESPACE
2a121ec5fafedd6d7872a2c217f32c47 *R/context.R
befb1350e0acf693cffb2f9a96b6f298 *R/diffPeaks.R
75c2c873eba43f9b15f2a1698c66e375 *R/filter.R
43943942297daac8bb6b5d457c6e5b40 *R/fraglen.R
e572fa354e7816755137b956ab8711e2 *R/intersect.R
a9ead99367d109dfbd5585b23ee337e6 *R/islands.R
a4c82d39eb49efdbdd3476145a020954 *R/peaks.R
ea83d721a373339e8a4740f80c652ad1 *R/plots.R
1f2f542e664d14853f125c6b405ef106 *R/subsets.R
44de30a288599c12148bd882176404bf *TODO
0ac47e25e2dbc7f0e5ccca1b31628ef5 *build/vignette.rds
64791505e1115873368a8b611504528e *data/cstest.rda
26d95dabd87acbdf44ecda045e2e6ec7 *data/datalist
c67ac49dbe2a5c389a1b642feed5cbc9 *inst/Scripts/AntibodyComparison.Rnw
630a273418c2f9ea72fc5134e7ec70dd *inst/Scripts/CTCFBindingSites.R
ca9cf8135dd0e90c84a79c7d25b67f8e *inst/Scripts/CTCF_ERV.R
aee97330bc6fc5325ce931bed2ce78db *inst/Scripts/CopyNumber.Rnw
b9fdf9ddd9d25837d91b84181d44a947 *inst/Scripts/Islands.Rnw
d3e0e7d6d67905e3f34b7b3115d6729a *inst/Scripts/MyoD.R
70ed9c49dec4afdb22fde785402b70ba *inst/Scripts/PairedEndComparison.Rnw
dcb4e37001f03145920d1c8ff3117e0f *inst/Scripts/PeakContextHuman.Rnw
e22d7dbd060325161369d0e7e2e58809 *inst/Scripts/PeakContextMouse.Rnw
bf012dbfcfee1aee1d476b131ff815b6 *inst/Scripts/PeakCutoff.Rnw
027314cba8b874dc1d337a24048faf6a *inst/Scripts/PeakModel.Rnw
10a39afb911fbcfd768ce3f473074e6e *inst/Scripts/PeakReproducibility.Rnw
fc5f8df77609407d4dde159745ead9de *inst/Scripts/PeaksByCopyNumber.Rnw
727166198a38cc8d25d326ca1eb40ec4 *inst/Scripts/RateComparison.Rnw
aa70f1fa6f051112a2d02f42a95ce676 *inst/Scripts/ReadAndSave54.R
ae7894a5b856dbaf4eb47efb18a37aaa *inst/Scripts/ReadAndSaveCTCF.R
42e617263ffdc34e7ca72e2812520574 *inst/Scripts/ReadAndSaveData.R
05caa000363574dcdbb4f33f43adc444 *inst/Scripts/ReadAndSaveSimulation.R
0499bfe7ca2da5b930300dcea653fe3f *inst/Scripts/SolexaSim.R
8418412635db910c56247de35566e5e9 *inst/Scripts/abc.rda
b2b3308f0d60517c9e1d4d10aadc2ac9 *inst/Scripts/antibody_comparison.R
ed4f51f8bcebaf4eeeb5c96ff4879c24 *inst/Scripts/dePeaks.R
f7d49434a22023a99f7926fb6ee4f6e6 *inst/Scripts/diffpeak.R
3ed9c551e8103a45b28b99eb559a484f *inst/Scripts/diffpeaks.R
837228bc953727b032e40cbb6205a57d *inst/Scripts/estimate_fragment_size.R
a06c7dabaad7ed64c565327650ca8cc9 *inst/Scripts/fibroblasts.R
e72faaaedf165cab4014877a5c052884 *inst/Scripts/getIsochores.R
3783000fdd3bf5e218849c3c4f13125f *inst/Scripts/hmm.R
4b7c58b557ccce7b42ccc011b4d82021 *inst/Scripts/human-islands.R
eeaf2ff4f62313033a80205dee813c86 *inst/Scripts/isochore_comparison.R
f7328263dd15bd2151f28b1608cbbb49 *inst/Scripts/isochores.mm9.rda
c7a667f5161cfde7f01daaa6d4caa464 *inst/Scripts/negbinomial.R
a2ca467d2433f490d5cc6b1343690bb2 *inst/Scripts/peakContext.R
786298cc4d4d8d7fba7ac8a3cdf3bdc5 *inst/Scripts/peak_mle.R
e14f736999fe4d70f015fb4d4e39ba68 *inst/Scripts/poisson.R
2d307d1468ebac6eea2f052f07bb4e30 *inst/Scripts/simulate.R
bf32b8fbb5ae9f6aca83195bf78deae3 *inst/Scripts/singletons.Rnw
41c6ab6fd784ed7445193929413afc97 *inst/Scripts/solexa54.R
6103d6a9c3d7663495c741be1fd665ec *inst/doc/Workflow.R
bafc924ea708e2ca2337797e51490748 *inst/doc/Workflow.Rmd
44d18a754bfe90b03df1464b8adc0af8 *inst/doc/Workflow.html
0050b633024e373d49b173695904a046 *man/chipseqFilter.Rd
fcbd69ee3a903e80390b7d15c55c9e85 *man/coverageplot.Rd
d87aaab400821fb0a6d24332643ffe48 *man/cstest.Rd
29ae87db043eb8a06bff04c8c28d031b *man/diffPeakSummary.Rd
6bbdbd6f9471746a54eeef97bf8628ce *man/estimate.mean.fraglen.Rd
b1666f6b83a6b6278f9c6baf189da6cc *man/islandDepthPlot.Rd
bb52d16ec9c782d59748c0f2198ea0c4 *man/laneSubsample.Rd
ee448a0edd9e15942dc914ab77a9f813 *man/peakCutoff.Rd
28f4b55e6e87073246f5a30a8f65deaf *man/peakSummary-methods.Rd
ee59e094ba8d95726351bb2360d5e0b1 *man/subsetSummary.Rd
4473cc6dd5867b7984f22884946a89d8 *src/rlesumprod.c
bafc924ea708e2ca2337797e51490748 *vignettes/Workflow.Rmd
